Chapter 6wtyler-irsc.weebly.com/uploads/1/9/8/6/19866611/chapt_06... · 2019-09-07 · Negative vs....

1

Energy and Metabolism

Chapter 6

2

Flow of Energy

• Thermodynamics

– Branch of chemistry

concerned with energy

changes

• Cells and biological

processes are governed

by the laws of physics

and chemistry

http://vinodwadhawan.blogspot.com/2011/12/5-can-you-unscramble-egg.html

• Energy – capacity to

do work

– Two states

1. Kinetic – energy of

motion

2. Potential – stored

energy

– Many forms –

mechanical, heat,

sound, electric current,

light, or radioactivity 3

http://www.petervaldivia.com/technology/energy/

4

a. Potential energy b. Kinetic energy

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

• Energy – capacity to do work

– Heat is the most convenient way of measuring

energy • 1 calorie = heat required to raise 1 gram of water 1ºC

• calorie or Calorie (= 1000 calories)?

5

Potential energy Kinetic energy

• Energy flows into the biological world from

the sun

– Photosynthetic organisms capture this energy

– Stored as potential energy in chemical bonds

6

http://utahscience.oremjr.alpine.k12.ut.us/sciber99/8th/energy/sciber/ecosys.htm

7

Redox reactions

• Oxidation

– Atom or molecule loses an

electron

• Reduction

– Atom or molecule gains an

electron

– Higher level of energy than

oxidized form

• Oxidation-reduction

reactions (redox)

– Reactions always paired

http://www.green-planet-solar-energy.com/oxidation-reduction-reactions.html

Potential Kinetic

Kinetic Potential

Reduction

Oxidation

8


e –

A B

A + B + A +

B –

Loss of electron (oxidation)

Gain of electron (reduction)

Lower energy Higher energy

Laws of thermodynamics

• First law of thermodynamics

– Energy cannot be created nor

destroyed

– Energy can only change from

one form to another

– Total amount of energy in the

universe remains constant

– During each conversion, some

energy is lost as heat

9

http://biology200.gsu.edu/houghton/2107%20%2713/lecture18.html

10

• Second law of

thermodynamics

– Entropy (disorder) is

continuously increasing

– Energy transformations

proceed spontaneously

to convert matter from a

more ordered/less stable

form to a less ordered/

more stable form

– Heat is lost from all

reactions http://biology200.gsu.edu/houghton/2107%20%2713/lecture18.html


Disorder happens

spontaneously

Organization

requires energy

© Jill Braaten

12

Free energy

• G = Energy available to do work (usable energy)

• G = H – TS

H = enthalpy, energy in a molecule’s chemical bonds

T = absolute temperature

S = entropy, unavailable energy (lost, unusable)

http://biology200.gsu.edu/houghton/2107%20%2713/lecture18.html

G S

H G = H – TS

ΔG = ΔH – TS • ΔG = change in free energy

• Positive ΔG – Products have more free energy than reactants

– H is higher or S is lower

– Endergonic

– Not spontaneous, requires input of energy

• Negative ΔG – Products have less free energy than reactants

– H is lower or S is higher or both

– Exergonic

– Spontaneous (may not be instantaneous),

– Releases energy

13

Fre

e e

nerg

y

Initial state

(reactants)

Final state

(products)

ΔG > 0

Fre

e e

nerg

y

Initial state

(reactants)

Final state

(products)

ΔG < 0

14


a.

b.

0

0

Course of Reaction

Products

G > 0

G < 0

Reactants

Reactants

Course of Reaction

Products

Fre

e E

nerg

y (

G)

En

erg

y R

ele

ase

d E

nerg

y S

up

plie

d

Fre

e E

nerg

y (

G)

En

erg

y R

ele

ase

d E

nerg

y S

up

plie

d

Energy is

released

Energy must

be supplied

Exergonic

Endergonic

Activation energy

• Extra energy (EA) required to

destabilize existing bonds and

initiate a chemical reaction

• Exergonic reaction’s rate depends

on the activation energy required

– Larger activation energy proceeds

more slowly

• Rate can be increased 2 ways

1. Increasing energy of reacting

molecules (heating)

2. Lowering activation energy

15

http://www4.nau.edu/meteorite/Meteorite/Book-GlossaryA.html

16


ΔG

En

erg

y R

ele

as

ed

En

erg

y S

up

plie

d

Fre

e E

ne

rgy (

G) Activation

energy

Activation

energy 0

uncatalyzed

catalyzed

Course of Reaction

Product

Reactant

Catalysts

• Substances that influence

chemical bonds in a way that

lowers activation energy

• Cannot violate laws of

thermodynamics

– Cannot make an endergonic

reaction spontaneous

• Do not alter the proportion of

reactant turned into product

17

http://www4.nau.edu/meteorite/Meteorite/Book-GlossaryA.html

18


ΔG

En

erg

y R

ele

as

ed

En

erg

y S

up

plie

d

Fre

e E

ne

rgy (

G) Activation

energy

Activation

energy 0

uncatalyzed

catalyzed

Course of Reaction

Product

Reactant

19

ATP

• Adenosine triphosphate

– Chief “energy currency” all cells use

– Composed of… • Ribose – 5 carbon sugar

• Adenine

• Chain of 3 phosphates – Key to energy storage

– Bonds are unstable

• ADP – 2 phosphates

• AMP – 1 phosphate – lowest energy form

http://chemwiki.ucdavis.edu/Physical_Chemistry/Thermodynamics/Case_Studies/Case_Study%3A_Thermodynamics_of_ATP

20


AM

P C

OR

E

O

O–

O

O

O

H H H

H

O

C C

N N

N

C

N

C

C H H

P O–

O P

O P O

AD

P

AT

P

Triphosphate

group

O–

CH2

High-energy

bonds

a.

Adenine NH2

Ribose

OH OH

b.

21

ATP cycle

• Exergonic ATP hydrolysis

drives coupled endergonic

reactions

– Coupled reaction results in net

–ΔG (exergonic & spontaneous)

• ATP not suitable for long-term

energy storage

– Fats and carbohydrates better

– Cells store only a few seconds

worth of ATP

22


+

+

Pi

Energy from

exergonic

cellular

reactions

ATP H2O

ADP

Energy for

endergonic

cellular

processes

23

Enzymes: Biological Catalysts

• Most enzymes are protein

– Some are RNA

• Shape of enzyme stabilizes a temporary association between substrates

• Enzyme not changed or consumed in reaction

http://www.ptj.com.pk/Web-2010/04-10/Muhammad-Ayaz-Shaikh.htm

24

Enzymes: Biological Catalysts

• Example: Carbonic anhydrase (enzyme used to maintain blood pH)

– 200 molecules of carbonic acid per hour made without enzyme

– 600,000 molecules formed per second with enzyme

• Most enzymes end in -ase

http://www.chem.harvard.edu/groups/shakhnovich/people/kutchukian.html

Active site

• Pockets or clefts for

substrate binding

• Precise fit of substrate into

active site

• Forms enzyme–substrate

complex

25

http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit6/genetics/proteins/enzymes/enzsub.html

Active site

• As the enzyme–substrate complex forms…

– The enzyme molecule changes shape slightly

(Induced fit) …

– Applies stress to distort particular bond to lower

activation energy to speed reaction

26 http://www.ptj.com.pk/Web-2010/04-10/Muhammad-Ayaz-Shaikh.htm

27


Active site

a. b.

Enzyme Enzyme–substrate complex

Substrate

28


1. The substrate, sucrose,

consists of glucose and

fructose bonded together.

2. The substrate binds to the active site

of the enzyme, forming an enzyme–

substrate complex.

3. The binding of the substrate and

enzyme places stress on the glucose–

fructose bond, and the bond breaks.

4. Products are

released, and

the enzyme is

free to bind other

substrates.

Bond Glucose

Fructose

Active site

Enzyme

sucrase

H2O

29

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30

• Enzymes may be suspended in the cytoplasm or attached to cell membranes and organelles

• Multienzyme complexes – subunits work together to form molecular machine – Product can be delivered easily to

next enzyme

– Unwanted side reactions prevented

– All reactions can be controlled as a unit

http://msb.bio.uni-goettingen.de/SFB860/Projects_b.html

31

Nonprotein enzymes

• Ribozymes

– 1981 discovery that certain reactions catalyzed in cells by RNA molecule itself

– Two kinds 1. Intramolecular catalysis –

catalyze reaction on RNA molecule itself

2. Intermolecular catalysis – RNA acts on another molecule

http://chemistry.gsu.edu/faculty/Huang/ribozyme.htm

Enzyme function

• Rate of enzyme-catalyzed

reaction depends on

concentrations of substrate

and enzyme (c)

• Any chemical or physical

condition that affects the

enzyme’s three-dimensional

shape can change rate…

– Optimum temperature (a)

– Optimum pH (b)

32

http://academic.pgcc.edu/~kroberts/Lecture/Chapter%205/enzymes.html

What is happening here??

33


a.

b.

Rate

of

Reacti

on

Optimum pH for pepsin

Rate

of

Reacti

on

pH of Reaction

Optimum pH for trypsin

1 2 3 4 5 6 7 8 9

30 40 50 60 70 80

Temperature of Reaction (˚C)

Optimum temperature

for human enzyme Optimum temperature for enzyme

from hotsprings prokaryote

What is happening here??

34

Inhibitors • Inhibitor – substance that

binds to enzyme and

decreases its activity

• Competitive inhibitor

– Competes with substrate for

active site

– Physically blocks active site

– Typically reversible

http://biochemanics.wordpress.com/tag/reversible-inhibitors/

35

Inhibitors

• Noncompetitive inhibitor

– Binds to enzyme at a site other

than active site (allosteric site)

– Causes shape change that

makes enzyme unable to bind

substrate

– Maybe irreversible (toxin) or

reversible (allosteric regulation)

http://biochemanics.wordpress.com/tag/reversible-inhibitors/

36

a. Competitive inhibition b. Noncompetitive inhibition

Enzyme Enzyme

Allosteric site

Active

site

Competitive inhibitor interferes

with active site of enzyme so

substrate cannot bind

Noncompetitive inhibitor changes

shape of enzyme so it cannot

bind to substrate

Active

site


Substrate Substrate

Inhibitor Inhibitor

37

Allosteric Enzymes

• Allosteric enzymes – enzymes exist in active

and inactive forms

• Most noncompetitive inhibitors bind to allosteric

site – chemical on/off switch

http://www.biology.arizona.edu/biochemistry/problem_sets/energy_enzymes_catalysis/03t.html

38

Allosteric Enzymes

• Allosteric inhibitor – binds to allosteric site and

reduces enzyme activity

• Allosteric activator – binds to allosteric site and

increases enzyme activity

http://www.biology.arizona.edu/biochemistry/problem_sets/energy_enzymes_catalysis/03t.html

39

Metabolism

• Total of all chemical reactions carried out by

an organism

– Anabolic reactions/anabolism

• Expend energy to build molecules

• Anabolic steroids = build muscle

– Catabolic reactions/catabolism

• Harvest energy by breaking down molecules

• Starvation = breaks down muscle

Larger

molecules

Smaller

molecules +

Energy and Energy

Conversions

• Summary of terms:

Catabolism Anabolism

Exergonic Endergonic

Kinetic Energy Potential Energy

Releases Stores

41

Biochemical pathways

• Chemical reactions

that create/store or

produce other

chemical products

for daily function

• Reactions occur in

a sequence

42

Biochemical pathways

• Product of one reaction is the substrate for the next reaction

• Some reactions such as glycolysis takes place in the cytoplasm; others such as the electron transport chain take place in organelles

• Enzymes in pathway maybe located within a single membrane


Initial substrate

Intermediate

substrate A

Intermediate

substrate B

Intermediate

substrate C

End product

Enzyme1

Enzyme2

Enzyme3

Enzyme4

Basic metabolic pathway chart

43

http://upload.wikimedia.org/wikipedia/commons/1/11/Metabolism_wip.png

http://upload.wikimedia.org/wikipedia/commons/1/11/Metabolism_wip.png

Feedback inhibition

• End-product of

pathway binds to an

allosteric site on

enzyme that catalyzes

first reaction in

pathway

• Shuts down pathway

so raw materials and

energy are not wasted

• Usually at or near first

step in pathway 44

b.

Enzyme 1

Enzyme 2

Enzyme 3 End product

Initial

substrate

45


a.

Enzyme 1

Enzyme 2


Initial

substrate

Intermediate

substrate A

Intermediate

substrate B

b.

Enzyme 1

Enzyme 2


Initial

substrate

Biochemical pathway

lacking feedback

Biochemical pathway

with negative feedback

Negative vs. Positive Feedback

• Negative feedback

(inhibition)

– Most common control type

– Downstream product

increases, this increase

level of product tells an

upstream factor that there is

enough and it slows or

stops the reaction.

• Blood pressure: standup fast,

HR increases to keep you

from passing out, then HR

returns to normal. 46

Blood pressure

decrease

Receptors in

carotids

Brain

Increase

heart rate

Negative vs. Positive Feedback

• Positive feedback – Very few examples in normal physiology that have a good

outcome

– Downstream product tells the upstream system that more needs to be produced

• Childbirth: control of the contractions, the harder the babies head pushes on the cervix causes hormones to be produced that increase the muscle contraction. This continues until baby and placenta are delivered.

47 http://kageeamy2012.wikispaces.com/01

+Homeostasis+%26+Chemical+Aspects

48

Please note that due to differing

operating systems, some animations

will not appear until the presentation is

viewed in Presentation Mode (Slide

Show view). You may see blank slides

in the “Normal” or “Slide Sorter” views.

All animations will appear after viewing

in Presentation Mode and playing each

animation. Most animations will require

the latest version of the Flash Player,

which is available at

http://get.adobe.com/flashplayer.

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